[gmx-users] Carbon Nanotube Force Field
spoel at xray.bmc.uu.se
Tue Aug 2 19:42:37 CEST 2005
On Tue, 2005-08-02 at 12:18 -0400, Bob Johnson wrote:
> I'm simulating a system involving carbon nanotubes. As an initial test of my
> force field I want to simulate a single infinite carbon nanotube. I've done
> simulations at constant volume and constant pressure. I've also run some energy
> minimizations. However, it seems that the energy is always too high and the tube
> wants to develop kinks and collapse on itself. I'm using the following force
> field obtained from the following paper: Guo, Karasawa, Goddard, Nature, Vol.
> 351, 1991
try to do it systematically. Turn off all interaction except the bonds
(remember to use pbc = full for infinite system).
If that behaves you add the next interaction. Turn off LJ by setting
nrexcl = 10 or something like that.
> Morse potential (function 3 in GROMACS)
> D = 478.9 kJ/mol
> b_0 = 0.1418 nm
> beta = 21.867 nm^-1
> G96 angle (function 2 in GROMACS)
> theta_0 = 120.00
> fc = 562.2 kJ/mol
Check fc, units are not correct.
> Proper dihedral (function 1 in GROMACS)
> theta_max = 180.00
> fc = 12.06 kJ/mol
> mult = 2
> L-J (function 1 in GROMACS)
> c6 = 4*eps*sig^6 = 5.7353e-3 kJ nm^6/mol
> c12 = 4*eps*sig^12 = 1.8707e-5 kJ nm^12/mol
> Can anyone verify that this is correct? Any suggestions on stabilizing the
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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